The genetic material forming the mitochondrial genome is similar in structure to that of the prokaryotic genetic material. The mitochondrial chromosome is a circular DNA molecule, but unlike prokaryotes it is much smaller and several copies are present. This similarity supports the hypothesis that mitochondria arose from intracellular bacterial symbiotes, i.e the endosymbiotic theory.

The mitochondria of a sexually-reproducing species are inherited maternally. In this way, mitochondrial genetic diseases can affect both males and females, but can only be transmitted by females to their offspring. The human mitochonrial genome consists of 16,569 base pairs, which encodes only 13 proteins, 22 tRNAs, and 2 rRNAs.

Compared to the nuclear genome, the mitochondrial genome possesses some very interesting features:

All the genes are carried on a single circular DNA molecule.

The genetic material is not bounded by a nuclear envelope.

The DNA is not packed with Chromatin.

The genome contains little non-coding DNA (junk DNA, or "introns").

Some codons do not follow the universal rules in translation. Instead they resemble those of purple nonsulfur bacteria.

Some bases are considered as a part of two different genes: as the last base of a gene and the first base of the next gene.